ClinVar Miner

Submissions for variant NM_170707.4(LMNA):c.936+2T>C

dbSNP: rs797045011
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Mendelics RCV000986430 SCV001135430 likely pathogenic Hutchinson-Gilford syndrome 2019-05-28 criteria provided, single submitter clinical testing
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario RCV001798660 SCV002041926 likely pathogenic Cardiomyopathy 2020-03-26 criteria provided, single submitter clinical testing
Ambry Genetics RCV003165426 SCV003855252 uncertain significance Cardiovascular phenotype 2022-11-02 criteria provided, single submitter clinical testing The c.936+2T>C intronic variant results from a T to C substitution two nucleotides after coding exon 5 in the LMNA gene. Alterations that disrupt the canonical splice site are expected to result in aberrant splicing. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. The resulting transcript is predicted to be in-frame and is not expected to trigger nonsense-mediated mRNAdecay; however, direct evidence is unavailable. The exact functional effect of the altered amino acid sequence is unknown. This nucleotide position is highly conserved in available vertebrate species. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Labcorp Genetics (formerly Invitae), Labcorp RCV003743622 SCV004376231 likely pathogenic Charcot-Marie-Tooth disease type 2 2023-09-27 criteria provided, single submitter clinical testing In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 208496). Disruption of this splice site has been observed in individual(s) with LMNA-related conditions (PMID: 23349452, 31038196). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 5 of the LMNA gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in LMNA are known to be pathogenic (PMID: 18585512, 18926329).

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